TRITON: in silico construction of protein mutants and prediction of their activities

PROKOP, Martin, Jiří DAMBORSKÝ and Jaroslav KOČA. TRITON: in silico construction of protein mutants and prediction of their activities. Bioinformatics. 2000, vol. 16, No 9, p. 845-846. ISSN 1367-4803.

Basic information

Original name

TRITON: in silico construction of protein mutants and prediction of their activities

Authors

PROKOP, Martin (203 Czech Republic), Jiří DAMBORSKÝ (203 Czech Republic) and Jaroslav KOČA (203 Czech Republic, guarantor)

Edition

Bioinformatics, 2000, 1367-4803

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Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.409

RIV identification code

RIV/00216224:14310/00:00002682

Organization unit

Faculty of Science

UT WoS

000165748700013

Keywords in English

HALOALKANE DEHALOGENASE; SUBSTRATE-SPECIFICITY; CATALYTIC MECHANISM

Tags

CATALYTIC MECHANISM, haloalkane dehalogenase, SUBSTRATE-SPECIFICITY

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Abstract

V originále

Motivation: One of the objectives of protein engineering is to propose and construct modified proteins with improved activity for the substrate of interest. Systematic computational investigation of many protein variants requires the preparation and handling of a large number of data files. The type of the data generated during the modelling of protein variants and the estimation of their activities offers the possibility of process automatization. Results: The graphical program TRITON has been developed for modelling protein mutants and assessment of their activities. Protein mutants are modelled from the wild type structure by homology modelling using the external program MODELLER. Chemical reactions taking place in the mutants active site are modelled using the semi-empirical quantum mechanic program MOPAC. Semi-quantitative predictions of mutants activities can be achieved by evaluating the changes in energies of the system and partial atomic charges of active site residues during the reaction. The program TRITON offers graphical tools for the preparation of the input data files, for calculation and for the analysis of the generated output data. Availability: The program TRITON can run under operating systems IRIX, Linux and NetBSD. The software is available at http://www.chemi.muni.cz/lbsd/triton.html.Contact: [e-mail]

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Links

GA203/97/P149, research and development project	Name: Studium molekulárních mechanismů biodegradačních reakcí - konstrukce QSBR modelů a proteinové inženýrství dehalogenas Investor: Czech Science Foundation, Study of the molecular mechanisms of biodegradation reactions - construction of QSBR models and protein engineering of haloalkane dehalogenases
ME 276, research and development project	Name: Racionální re-design mikrobiálních enzymů podílejících se na degradaci toxických organických polutantů Investor: Ministry of Education, Youth and Sports of the CR, Rational re-design of microbial enzymes involved in degradation of toxic organic pollutants.
MSM 143100005, plan (intention)	Name: Strukturně-funkční vztahy biomolekul a jejich role v metabolismu Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular Structure-function Relationships and their role in the Metabolism